Dissolved organic matter (DOM) represents a key component of carbon (C) cycling in freshwater ecosystems. While the behaviour of bulk dissolved organic carbon (DOC) in aquatic ecosystems is well studied, comparatively little is known about the turnover of specific DOC compounds. The aim of this study was to investigate the persistence of 14C-labelled low molecular weight (LMW) DOC at a wide range of concentrations (0.1 µM to 10 mM), in sediments and waters from oligotrophic and mesotrophic rivers within the same catchment. Overall, rates of DOC loss varied between compound groups (amino acids > sugars = organic acids > phenolics). Sediment-based microbial communities contributed to higher DOC loss from river waters, which was attributed, in part, to its greater microbial biomass. At higher DOC compound concentrations, DOC loss was greater in mesotrophic rivers in comparison to oligotrophic headwaters. A lag-phase in substrate use within sediments provided evidence of microbial growth and adaptation, ascribed here to the lack of inorganic nutrient limitation on microbial C processing in mesotrophic communities. We conclude that the higher microbial biomass and available inorganic nutrients in sediments enables the rapid processing of LMW DOC, particularly during high C enrichment events and in N and P-rich mesotrophic environments.